Mammalian genomes contain multiple copies of retroviral-related sequences. The majority of these are defective for virus expression; however, some can produce subgenomic RNAs. Age- dependent expression of endogenous retroviral sequences was studied in Mus musculus wild mouse and man using endogenous MuLV and human 4-1 DNA probes. In both cases transcripts were detected in kidney, brain, and liver tissues, but expression was highest in the kidney. MuLV-related RNAs, 8.4 kb, 3.0 kb, and 1.8 kb were seen throughout life (18 day old embryo - 28 months of age) and increased with age. Transcripts, 3.0 kb and 1.8 kb, were seen in human tissues from 8 month fetus -85 years of age. These RNAs also appeared to increase with age. The results suggest a relaxation of gene control in mammalian cells with aging. A novel 5.0 kb retrotransponson-like element, B-13, was cloned from BALB/c mouse embryo DNA and sequenced. It was distantly related to known MuLV DNAs: <75% homology was seen in the gag and pol regions; env sequences were absent. Two other cloned DNAs isolated from the BALB/c mouse genome contained B-13-like genes but different flanking cellular sequences. Several copies of B-13- related genes were detected in inbred and closely related wild mouse genomes. These results indicate that B-13-like elements are amplified and dispersed in the mouse genome. Two novel protein binding sites were identified at the 5' end of all MuLV-related LTRs using 30 bp oligomers as probes in gel mobility shift assays. These highly conserved sites were present upstream of the enhancer in a region designated as the upstream conserved region (UCR) and bound nuclear factors designated as UCRF-L and UCRF-U. UCRF-L was the prominent species in murine tissue whereas UCRF-U predominated in cell lines. Northern analysis of 5 different mouse strains indicated a good inverse correlation between MuLV RNA expression and UCRF-L activity. This relationship was seen in case of both spontaneous and LPS-induced MuLV RNAs. These results suggest a negative regulatory function of UCRF-L in MuLV gene expression.